The khmer software package: enabling efficient nucleotide sequence analysis

Michael R Crusoe; Hussien F Alameldin; Sherine Awad; Elmar Boucher; Adam Caldwell; Reed Cartwright; Amanda Charbonneau; Bede Constantinides; Greg Edvenson; Scott Fay; Jacob Fenton; Thomas Fenzl; Jordan Fish; Leonor Garcia-Gutierrez; Phillip Garland; Jonathan Gluck; Iván González; Sarah Guermond; Jiarong Guo; Aditi Gupta; Joshua R Herr; Adina Howe; Alex Hyer; Andreas Härpfer; Luiz Irber; Rhys Kidd; David Lin; Justin Lippi; Tamer Mansour; Pamela McA'Nulty; Eric McDonald; Jessica Mizzi; Kevin D Murray; Joshua R Nahum; Kaben Nanlohy; Alexander Johan Nederbragt; Humberto Ortiz-Zuazaga; Jeramia Ory; Jason Pell; Charles Pepe-Ranney; Zachary N Russ; Erich Schwarz; Camille Scott; Josiah Seaman; Scott Sievert; Jared Simpson; Connor T Skennerton; James Spencer; Ramakrishnan Srinivasan; Daniel Standage; James A Stapleton; Susan R Steinman; Joe Stein; Benjamin Taylor; Will Trimble; Heather L Wiencko; Michael Wright; Brian Wyss; Qingpeng Zhang; En Zyme; C Titus Brown

doi:10.12688/f1000research.6924.1

The khmer software package: enabling efficient nucleotide sequence analysis

F1000Res. 2015 Sep 25:4:900. doi: 10.12688/f1000research.6924.1. eCollection 2015.

Authors

Michael R Crusoe¹, Hussien F Alameldin², Sherine Awad³, Elmar Boucher⁴, Adam Caldwell⁵, Reed Cartwright⁶, Amanda Charbonneau⁷, Bede Constantinides⁸, Greg Edvenson⁹, Scott Fay¹⁰, Jacob Fenton¹¹, Thomas Fenzl¹², Jordan Fish¹¹, Leonor Garcia-Gutierrez¹³, Phillip Garland¹⁴, Jonathan Gluck¹⁵, Iván González¹⁶, Sarah Guermond¹⁷, Jiarong Guo¹⁸, Aditi Gupta¹, Joshua R Herr¹, Adina Howe¹⁹, Alex Hyer²⁰, Andreas Härpfer²¹, Luiz Irber¹¹, Rhys Kidd²², David Lin²³, Justin Lippi²⁴, Tamer Mansour²⁵, Pamela McA'Nulty²⁶, Eric McDonald¹¹, Jessica Mizzi²⁷, Kevin D Murray²⁸, Joshua R Nahum²⁹, Kaben Nanlohy³⁰, Alexander Johan Nederbragt³¹, Humberto Ortiz-Zuazaga³², Jeramia Ory³³, Jason Pell¹¹, Charles Pepe-Ranney³⁴, Zachary N Russ³⁵, Erich Schwarz³⁶, Camille Scott¹¹, Josiah Seaman³⁷, Scott Sievert³⁸, Jared Simpson³⁹, Connor T Skennerton⁴⁰, James Spencer⁴¹, Ramakrishnan Srinivasan⁴², Daniel Standage⁴³, James A Stapleton⁴⁴, Susan R Steinman⁴⁵, Joe Stein⁴⁶, Benjamin Taylor¹¹, Will Trimble⁴⁷, Heather L Wiencko⁴⁸, Michael Wright¹¹, Brian Wyss¹¹, Qingpeng Zhang¹¹, En Zyme⁴⁹, C Titus Brown⁵⁰

Affiliations

¹ Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
² Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
³ Population Health and Reproduction, University of California, Davis, Davis, CA, USA.
⁴ Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
⁵ Biology Department, San Jose State University, San Jose, CA, USA.
⁶ School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
⁷ Genetics, Michigan State University, East Lansing, MI, USA.
⁸ Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
⁹ Micron Technology, Seattle, WA, USA.
¹⁰ Invitae, San Francisco, CA, USA.
¹¹ Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
¹² Independent Researcher, Munich, Germany.
¹³ Mathematics Institute, University of Warwick, Warwick, UK.
¹⁴ Eastlake Data, Seattle, WA, USA.
¹⁵ Graduate Program, University of Maryland, College Park, MD, USA.
¹⁶ Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA.
¹⁷ Independent Researcher, Seattle, WA, USA.
¹⁸ Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
¹⁹ Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA.
²⁰ Department of Biology, University of Utah, Salt Lake City, UT, USA.
²¹ ConSol Software GmbH, Munchen, Germany.
²² Independent Researcher, Sydney, Australia.
²³ Verdematics, Fremont, CA, USA.
²⁴ Independent Researcher, San Francisco, CA, USA.
²⁵ Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; Clinical Pathology, Mansoura University, Mansoura, Egypt.
²⁶ Addgene, Cambridge, MA, USA.
²⁷ Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
²⁸ ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia.
²⁹ BEACON Center, Michigan State University, East Lansing, MI, USA.
³⁰ Independent Researcher, New Orleans, LA, USA.
³¹ Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway.
³² Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico.
³³ Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA.
³⁴ Crop and Soil Sciences, Cornell University, Ithaca, NY, USA.
³⁵ Department of Bioengineering, UC Berkeley, Berkeley, CA, USA.
³⁶ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
³⁷ Data Visualization, Newline Technical Innovations, Windsor, CO, USA.
³⁸ Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA.
³⁹ Ontario Institute for Cancer Research, Toronto, ON, Canada ; Computer Science, University of Toronto, Toronto, ON, Canada.
⁴⁰ Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
⁴¹ Dept of Physics and Dept of Materials, Imperial College London, London, UK.
⁴² Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁴³ Department of Biology, Indiana University, Bloomington, IN, USA ; Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA.
⁴⁴ Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USA.
⁴⁵ The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA.
⁴⁶ Independent Researcher, Providence, RI, USA.
⁴⁷ Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA.
⁴⁸ Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland.
⁴⁹ Independent Researcher, Boston, MA, USA.
⁵⁰ Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA ; Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.

Abstract

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

Keywords: bioinformatics; dna sequencing analysis; k-mer; khmer; kmer; low-memory; online; streaming.

Grants and funding

R01 HG007513/HG/NHGRI NIH HHS/United States